Frank-thomas Koch - Academia.edu (original) (raw)

Papers by Frank-thomas Koch

. Understanding of regional greenhouse gas emissions into the atmosphere is a prerequisite to mit... more . Understanding of regional greenhouse gas emissions into the atmosphere is a prerequisite to mitigate climate change. In this study, we investigated the regional contributions of carbon dioxide (CO2) at the location of the high Alpine observatory Jungfraujoch ("JFJ", Switzerland, 3580 m a.s.l.). To this purpose, we combined receptor-oriented atmospheric transport simulations for CO2 concentration in the period of 2009–2017 with stable carbon isotope (δ13C-CO2) information. We applied two Lagrangian particle dispersion models driven by output from two different numerical weather prediction systems (FLEXPART-COSMO and STILT-ECMWF) in order to simulate CO2 concentration at JFJ based on regional CO2 fluxes, to estimate atmospheric δ13C-CO2, and to obtain model-based estimates of the mixed source signatures (δ13Cm). Anthropogenic fluxes were taken from a fuel type-specific version of the EDGAR v4.3 inventory and ecosystem fluxes were based on the Vegetation Photosynthesis and Respiration Model (VPRM). The simulations of CO2, δ13C-CO2 and δ13Cm were then compared to observations performed by quantum cascade laser absorption spectroscopy. Around 40 % of the regional CO2 variability above or below the large-scale background was captured by the models, and up to 35 % of the regional variability in δ13C-CO2. This is remarkable considering the complex Alpine topography, the low intensity of regional signals at JFJ, and the challenging measurements. Best agreement between simulations and observations in terms of short-term variability and intensity of the signals for CO2 and δ13C-CO2 was found between late autumn and early spring. The agreement was inferior in the early autumn periods and during summer. This may be associated with the atmospheric transport representation in the models. In addition, the net ecosystem exchange fluxes are a possible source of error, either through inaccuracies in their representation in VPRM for the (Alpine) vegetation or through a day (uptake) vs. night (respiration) transport discrimination to JFJ. Furthermore, the simulations suggest that JFJ is subject to relatively small regional anthropogenic contributions, due to its remote location (elevated and far from major anthropogenic sources), and the limited planetary boundary layer-influence during winter. Instead, the station is primarily exposed to summer-time ecosystem CO2 contributions, which are dominated by rather nearby sources (within 100 km). Even during winter, simulated gross ecosystem respiration accounted for approximately 50 % of all contributions to the CO2 concentrations above the largescale background. The model-based monthly mean δ13Cm ranged from −22 ‰ in winter to −28 ‰ in summer and reached the most depleted values of −35 ‰ at higher fractions of natural gas combustion, and the most enriched values of −17 to −12 ‰ when impacted by cement production emissions. Observation-based δ13Cm values derived by a moving Keeling-plot approach were in good agreement with the model-based estimates. They exhibited a larger scatter, while model-based estimates spread in a more narrow range. Overall, observation-based δ13Cm were limited to a smaller number of data points compared to model-based estimates owing to the stringent analysis prerequisites in combination with the low regional signal at JFJ.

<p>... more <p>With an increasing network of atmospheric stations that produce a constant data stream, top-down inverse transport modelling of GHGs in a quasi-operational way becomes feasible. The CarboScope-Regional inversion system embeds the regional inversion, within a global inversion using the two-step approach. The regional inversion consists of Lagrangian mesoscale transport from STILT, prior fluxes from the diagnostic VPRM biosphere model, and anthropogenic emissions from a combination of EDGAR v4.3 with the annually updated BP statistical report. Regional ocean fluxes were derived from the CarboScope ocean flux product based on SOCATv2019 data. The inversion uses atmospheric observations from 44 stations to infer biosphere-atmosphere exchange. The regional domain covers most of Europe (33 – 73N, 15W – 35E) with a spatial resolution of 0.25 degree for fluxes and 0.5 degree for flux corrections inferred by the inversion (i.e. the state space).<br>One of the critical parameters is the assumed uncertainty of the observations, and the major contribution to this is the model-data mismatch error, or representation error. Within CarboScope-Regional, this model-data mismatch error is specified differently for different station types, such as tall towers, mountain or coastal stations, etc. To evaluate the validity and appropriateness of these assumed uncertainties, a leave-one-out cross-validation is applied for a single year, using all stations except one for the inversion, and comparing posterior concentrations predicted for the omitted station with the observed concentrations. Results of this cross-validation will be presented separately for the different station types, and will be used to evaluate the magnitude of the assumed model-data mismatch errors.</p>

<p>... more <p>Regional flux estimates over Europe have been calculated using the two-step inverse system of the Jena CarboScope Regional inversion (CSR) to estimate the annual CO<sub>2</sub> budgets for recent years, in cooperation with the research project VERIFY. The CSR system assimilates observational datasets of CO<sub>2</sub> mixing ratio provided by the Integrated Carbon Observation System (ICOS) across the European domain to optimize Net Ecosystem Exchange (NEE) fluxes computed from biosphere models at a spatial resolution of 0.25 degree. Ocean fluxes are assumed to be constant over time. Fossil fuel emissions are obtained from EDGAR_v4.3 and updated based on British Petroleum (BP) statistics. Therefore, only biosphere-atmosphere exchange fluxes are considered to be optimized against the atmospheric data.</p><p>In this study we focus on the impact of using a-priori fluxes from different biosphere and ocean models on the annual CO<sub>2</sub> budget of posterior fluxes. Results calculated using the Vegetation and Photosynthesis Respiration Model (VPRM) and Simple Biosphere/Carnegie-Ames Stanford Approach (SiBCASA) models show a consistent posterior interannual variability, largely independent of which prior fluxes are used, even though those prior fluxes show considerable differences on annual scales.</p>

<p class=&... more <p class="p1"><span class="s1">Due to the growth of atmospheric methane and the remarkable uncertainties in its budget, there is a need to constrain the sources and sinks of this atmospheric tracer. Among the different regions emitting methane to the atmosphere, Africa has a considerable contribution to the global methane budget and has one of the largest associated uncertainties. Surface-based measurements could help to substantially diminish these uncertainties, but given the dearth of in-situ observations in most areas of Africa, satellite retrievals can be helpful to fill this gap. We use ground-based observations along with the SRON’s proxy and full physics XCH</span><span class="s2"><sub>4</sub></span><span class="s1"> products from the Greenhouse Gases Observing Satellite (GOSAT), and an inversion system consisting of the global 3-dimensional transport model TM3 as well as the high-resolution regional Stochastic Time-Inverted Lagrangian Transport model STILT to spatially resolve the regional emissions in Africa with a focus on the natural wetlands and also the oil and gas industries in Nigeria and Angola as the top oil-producing African countries. In this study, the global inversion is performed for 2009-2015 on a coarse resolution, ~ 3.83˚ x 5˚. The nominal spatial resolution of the regional inversion is 0.25˚ x 0.25˚ for 2011-2012. Prior fluxes for the nested run include the Emission Database for Global Atmospheric Research (EDGARv4.3.2) for anthropogenic sources including agriculture, and waste and energy, WetCHARTs wetlands ensemble, the Global Fire Assimilation System (GFAS) for biomass burning, Sanderson’s global database of termite methane emissions, and the soil Methanotrophy Model (MeMo) for the methane soil uptake. The significance of the petroleum industries’ emissions is examined by high-resolution inversions. Additionally, the consistency of the optimised fluxed derived from different types of measurements (e.g. surface-only, surface+satellite, satellite-only) is investigated and discussed.</span></p>

<p&amp... more <p>During May and June 2018, the intensive campaign CoMet (Carbon dioxide and Methane mission) made atmospheric measurements of greenhouse gases over Europe, with the upper Silesian coal basin (USCB) in southern Poland as a specific focus area. CoMet aimed at characterising the distribution of CH<sub>4</sub> and CO<sub>2</sub> over significant regional sources with the use of a fleet of research aircraft, as well as to validate remote sensing measurements from state-of-the-art instrumentation installed on-board against a set of independent in-situ observations.</p> <p>In order to link atmospheric mixing ratios to source emission rates, high-resolution simulations with WRF-GHG v 3.9.1.1. (10 km x10 km Europe + nested 2 km x 2 km domain over the USCB), driven by short-term meteorological forecasts from the ECMWF IFS model and forecasts from CAMS (Copernicus Atmospheric Monitoring Service) for initial and lateral tracer boundary conditions were performed. Biogenic fluxes of CO2 were calculated online using the VPRM model driven by MODIS indices. Anthropogenic emissions over Europe were taken from the database of TNO, Department of Climate, Air and Sustainability (7 km x 7 km), augmented with an internal emissions database developed within CoMet that uses coal mine ventilation shaft emission measurements in combination with recent updates of the E-PRTR (European Pollutant Release and Transfer Register).</p> <p>Tagged tracers were used to simulate a robust set of over 100 distinct anthropogenic sources of CH<sub>4</sub> and CO<sub>2</sub> from the study area, and these forward simulations were then used as the transport operator in an analytical Bayesian inversion system. Here we discuss the results of an analysis performed with the use of selected in-situ data measured over the course of the three-week campaign, including results and sensitivity tests.</p>

Atmospheric inversions are widely used in the optimization of surface carbon fluxes at regional s... more Atmospheric inversions are widely used in the optimization of surface carbon fluxes at regional scale using information from atmospheric CO 2 dry mole fractions. In many studies the prior flux uncertainty applied to the inversion schemes does not reflect directly the true flux uncertainties but it is used in such a way to regularize the inverse problem. Here, we aim to implement an inversion scheme using the Jena inversion system and applying a prior flux error structure derived from a model-data residual analysis using high spatial and temporal resolution over a full year period in the European domain. We analyzed the performance of the inversion system with a synthetic experiment, where the flux constraint is derived following the same residual analysis but applied to the model-model mismatch. The synthetic study showed a quite good agreement between posterior and "true" fluxes at European/Country and annual/monthly scales. Posterior monthly and country aggregated fluxes improved their correlation coefficient with the "known truth" by 7% compared to the prior estimates when compared to the reference, with a mean correlation of 0.92. Respectively, the ratio of the standard deviation between posterior/reference and prior/reference was also reduced by 33% with a mean value of 1.15. We identified temporal and spatial scales where the inversion system maximizes the derived information; monthly temporal scales at around 200 km spatial resolution seem to maximize the information gain.

Optimized biogenic carbon fluxes for Europe were estimated from high resolution regional scale in... more Optimized biogenic carbon fluxes for Europe were estimated from high resolution regional scale inversions, utilizing atmospheric CO 2 measurements at 16 stations for the year 2007. Additional sensitivity tests with different data-driven error structures were performed. As the atmospheric network is rather sparse and consequently contains large spatial gaps, we use a priori biospheric fluxes to further constrain the inversions. The biospheric fluxes were simulated by the Vegetation Photosynthesis and Respiration Model (VPRM) at a resolution of 0.1º and optimized against Eddy covariance data. Overall we estimate an a priori uncertainty of 0.54 GtC y-1 related to the poor spatial representation between the biospheric model and the ecosystem sites. The sink estimated from the atmospheric inversions for the area of Europe (as represented in the model domain) ranges between 0.23 and 0.38 GtC y-1 (0.30 and 0.49 GtC y-1 up-scaled to geographical Europe). This is within the range of posterior flux uncertainty estimates of previous studies using ground based observations.

Atmospheric Measurement Techniques Discussions

The carbon exchange between ecosystems and the atmosphere has a large influence on the Earth syst... more The carbon exchange between ecosystems and the atmosphere has a large influence on the Earth system and specifically on the climate. This exchange is therefore being studied intensively, often using the eddy covariance (EC) technique. EC measurements provide reliable results under turbulent atmospheric conditions, but under stable conditions-as they often occur at night-these measurements are known to misrepresent exchange fluxes. Nocturnal boundary layer (NBL) budgets can provide independent flux estimates under stable conditions, but their application so far has been limited by rather high cost and practical difficulties. Unmanned aircraft systems (UASs) equipped with trace gas analysers have the potential to make this method more accessible. We present the methodology and results of a proof of concept study carried out during the ScaleX 2016 campaign. Successive vertical profiles of carbon dioxide dry air mole fraction in the NBL were taken with a compact analyser carried by a UAS. We estimate an average carbon dioxide flux of 12 µmol • m −2 • s −1 , which is plausible for nocturnal respiration in this region in summer. Transport modelling suggests that the NBL budgets represent an area on the order of 100 km².

Atmospheric Chemistry and Physics

Optimized biogenic carbon fluxes for Europe were estimated from high-resolution regional-scale in... more Optimized biogenic carbon fluxes for Europe were estimated from high-resolution regional-scale inversions, utilizing atmospheric CO 2 measurements at 16 stations for the year 2007. Additional sensitivity tests with different datadriven error structures were performed. As the atmospheric network is rather sparse and consequently contains large spatial gaps, we use a priori biospheric fluxes to further constrain the inversions. The biospheric fluxes were simulated by the Vegetation Photosynthesis and Respiration Model (VPRM) at a resolution of 0.1 • and optimized against eddy covariance data. Overall we estimate an a priori uncertainty of 0.54 GtC yr −1 related to the poor spatial representation between the biospheric model and the ecosystem sites. The sink estimated from the atmospheric inversions for the area of Europe (as represented in the model domain) ranges between 0.23 and 0.38 GtC yr −1 (0.39 and 0.71 GtC yr −1 up-scaled to geographical Europe). This is within the range of posterior flux uncertainty estimates of previous studies using groundbased observations.

Atmospheric Chemistry and Physics

Atmospheric inversions are widely used in the optimization of surface carbon fluxes on a regional... more Atmospheric inversions are widely used in the optimization of surface carbon fluxes on a regional scale using information from atmospheric CO 2 dry mole fractions. In many studies the prior flux uncertainty applied to the inversion schemes does not directly reflect the true flux uncertainties but is used to regularize the inverse problem. Here, we aim to implement an inversion scheme using the Jena inversion system and applying a prior flux error structure derived from a model-data residual analysis using high spatial and temporal resolution over a full year period in the European domain. We analyzed the performance of the inversion system with a synthetic experiment, in which the flux constraint is derived following the same residual analysis but applied to the model-model mismatch. The synthetic study showed a quite good agreement between posterior and "true" fluxes on European, country, annual and monthly scales. Posterior monthly and country-aggregated fluxes improved their correlation coefficient with the "known truth" by 7 % compared to the prior estimates when compared to the reference, with a mean correlation of 0.92. The ratio of the SD between the posterior and reference and between the prior and reference was also reduced by 33 % with a mean value of 1.15. We identified temporal and spatial scales on which the inversion system maximizes the derived information; monthly temporal scales at around 200 km spatial resolution seem to maximize the information gain.

Journal of Chemistry, 2015

Polarization of atoms plays a substantial role in molecular interactions. Class I and II force fi... more Polarization of atoms plays a substantial role in molecular interactions. Class I and II force fields mostly calculate with fixed atomic charges which can cause inadequate descriptions for highly charged molecules, for example, ion channels or metalloproteins. Changes in charge distributions can be included into molecular mechanics calculations by various methods. Here, we present a very fast computational quantum mechanical method, the Bond Polarization Theory (BPT). Atomic charges are obtained via a charge calculation method that depend on the 3D structure of the system in a similar way as atomic charges ofab initiocalculations. Different methods of population analysis and charge calculation methods and their dependence on the basis set were investigated. A refined parameterization yielded excellent correlation ofR=0.9967. The method was implemented in the force field COSMOS-NMR and applied to the histidine-tryptophan-complex of the transmembrane domain of the M2 protein channel o...

Lagrangian Modeling of the Atmosphere, 2012

Journal of Geophysical Research, 2012

Tropical regions, especially the Amazon region, account for large emissions of methane (CH 4). He... more Tropical regions, especially the Amazon region, account for large emissions of methane (CH 4). Here, we present CH 4 observations from two airborne campaigns conducted within the BARCA (Balanço Atmosférico Regional de Carbono na Amazônia) project in the Amazon basin in November 2008 (end of the dry season) and May 2009 (end of the wet season). We performed continuous measurements of CH 4 onboard an aircraft for the first time in the Amazon region, covering the whole Amazon basin with over 150 vertical profiles between altitudes of 500 m and 4000 m. The observations support the finding of previous ground-based, airborne, and satellite measurements that the Amazon basin is a large source of atmospheric CH 4. Isotope analysis verified that the majority of emissions can be attributed to CH 4 emissions from wetlands, while urban CH 4 emissions could be also traced back to biogenic origin. A comparison of five TM5 based global CH 4 inversions with the observations clearly indicates that the inversions using SCIAMACHY observations represent the BARCA observations best. The calculated CH 4 flux estimate obtained from the mismatch between observations and TM5-modeled CH 4 fields ranges from 36 to 43 mg m À2 d À1 for the Amazon lowland region.

Atmospheric Chemistry and Physics, 2011

Accurate simulation of the spatial and temporal variability of tracer mixing ratios over complex ... more Accurate simulation of the spatial and temporal variability of tracer mixing ratios over complex terrain is challenging, but essential in order to utilize measurements made in complex orography (e.g. mountain and coastal sites) in an atmospheric inverse framework to better estimate regional fluxes of these trace gases. This study investigates the ability of high-resolution modeling tools to simulate meteorological and CO 2 fields around Ochsenkopf tall tower, situated in Fichtelgebirge mountain range-Germany (1022 m a.s.l.; 50 • 1 48" N, 11 • 48 30" E). We used tower measurements made at different heights for different seasons together with the measurements from an aircraft campaign. Two tracer transport models-WRF (Eulerian based) and STILT (Lagrangian based), both with a 2 km horizontal resolution-are used together with the satellite-based biospheric model VPRM to simulate the distribution of atmospheric CO 2 concentration over Ochsenkopf. The results suggest that the high-resolution models can capture diurnal, seasonal and synoptic variability of observed mixing ratios much better than coarse global models. The effects of mesoscale transports such as mountain-valley circulations and mountain-wave activities on atmospheric CO 2 distributions are reproduced remarkably well in the high-resolution models. With this study, we emphasize the potential of using high-resolution models in the context of inverse modeling frameworks to utilize measurements provided from mountain or complex terrain sites.

First results from EUROCOM is not better than that obtained in state-of-the-art global inversions... more First results from EUROCOM is not better than that obtained in state-of-the-art global inversions. However, more robust results are obtained for subregions within Europe, and in these areas with dense observational coverage, the objective of delivering robust countryscale flux estimates appears achievable in the near future.

Briefings in functional genomics & proteomics, 2007

The rapidly increasing amount of information on three-dimensional (3D) structures of biological m... more The rapidly increasing amount of information on three-dimensional (3D) structures of biological macro-molecules has still an insufficient impact on genome analysis, functional genomics and proteomics as well as on many other fields in biomedicine including disease-related research. There are, however, attempts to make structural data more easily accessible to the bench biologist. As members of the world-wide Protein Data Bank (wwPDB), the RCSB Protein Data Bank (PDB), the Protein Data Bank Japan and the Macromolecular Structure Database are the primary information resources for 3D structures of proteins, nucleic acids, carbohydrates and complexes thereof. In addition, a number of secondary resources have been set up that also provide information on all currently known structures in a relatively comprehensive manner and not focusing on specific features only. They include PDBsum, the OCA browser-database for protein structure/function, the Molecular Modeling Database and the Jena Lib...

Macromolecular Chemistry and Physics, 2000

. Static 13 C powder pattern of the carbons in cellulose II obtained from the crystal structure (... more . Static 13 C powder pattern of the carbons in cellulose II obtained from the crystal structure (thin line) and after time averaging of the tensors obtained by MD simulations (fat line).

Journal of Computational Chemistry, 1994

ABSTRACT Starting from the bond polarization theory (BPT), a new semiempirical method for the cal... more ABSTRACT Starting from the bond polarization theory (BPT), a new semiempirical method for the calculation of net atomic charges is developed. The bond polarization theory establishes a linear dependence of atomic charges from the bond polarization energy. This energy is calculated from the hybrid orbitals forming a bond and the point charges within the neighborhood. Empirical parameters are introduced for the polarity of an unpolarized bond and for the change of the atomic charge with σ- and π-bond polarization. Because these parameters are linear, they can be calibrated directly using net atomic charges from ab initio calculations. This procedure was performed using the charges from STO3G calculations on a set of 18 amino acids. Using the two parameters for CH, OH, σ-CO, and NH bonds and the three parameters for CC, CO, and CN bonds, the 350 ab initio charges can be reproduced with high accuracy by solving sets of linear equations for the charges. The calculation of charges for large molecular systems including all inter- and intramolecular mutual polarizations requires only a few seconds (up to 100 atoms) or minutes (700 atoms) on a PC. This procedure is well suited for the application in molecular mechanics or molecular dynamics programs to overcome the limitations of most force fields used up to now. One of the weakest points in these programs is the use of fixed or topological charges to define the electrostatic potential. As an application of the new method, we calculated the interaction energy of an ion with valinomycin. This ring molecule forms octahedral oxygen cages around ions like potassium and acts thereby as selective ion carrier. To accomplish this function, valinomycin has to strip off the hydratization spheres of the ions, and therefore its preference for certain types of ions could be deduced from the interaction energies. © 1994 by John Wiley & Sons, Inc.

. Understanding of regional greenhouse gas emissions into the atmosphere is a prerequisite to mit... more . Understanding of regional greenhouse gas emissions into the atmosphere is a prerequisite to mitigate climate change. In this study, we investigated the regional contributions of carbon dioxide (CO2) at the location of the high Alpine observatory Jungfraujoch ("JFJ", Switzerland, 3580 m a.s.l.). To this purpose, we combined receptor-oriented atmospheric transport simulations for CO2 concentration in the period of 2009–2017 with stable carbon isotope (δ13C-CO2) information. We applied two Lagrangian particle dispersion models driven by output from two different numerical weather prediction systems (FLEXPART-COSMO and STILT-ECMWF) in order to simulate CO2 concentration at JFJ based on regional CO2 fluxes, to estimate atmospheric δ13C-CO2, and to obtain model-based estimates of the mixed source signatures (δ13Cm). Anthropogenic fluxes were taken from a fuel type-specific version of the EDGAR v4.3 inventory and ecosystem fluxes were based on the Vegetation Photosynthesis and Respiration Model (VPRM). The simulations of CO2, δ13C-CO2 and δ13Cm were then compared to observations performed by quantum cascade laser absorption spectroscopy. Around 40 % of the regional CO2 variability above or below the large-scale background was captured by the models, and up to 35 % of the regional variability in δ13C-CO2. This is remarkable considering the complex Alpine topography, the low intensity of regional signals at JFJ, and the challenging measurements. Best agreement between simulations and observations in terms of short-term variability and intensity of the signals for CO2 and δ13C-CO2 was found between late autumn and early spring. The agreement was inferior in the early autumn periods and during summer. This may be associated with the atmospheric transport representation in the models. In addition, the net ecosystem exchange fluxes are a possible source of error, either through inaccuracies in their representation in VPRM for the (Alpine) vegetation or through a day (uptake) vs. night (respiration) transport discrimination to JFJ. Furthermore, the simulations suggest that JFJ is subject to relatively small regional anthropogenic contributions, due to its remote location (elevated and far from major anthropogenic sources), and the limited planetary boundary layer-influence during winter. Instead, the station is primarily exposed to summer-time ecosystem CO2 contributions, which are dominated by rather nearby sources (within 100 km). Even during winter, simulated gross ecosystem respiration accounted for approximately 50 % of all contributions to the CO2 concentrations above the largescale background. The model-based monthly mean δ13Cm ranged from −22 ‰ in winter to −28 ‰ in summer and reached the most depleted values of −35 ‰ at higher fractions of natural gas combustion, and the most enriched values of −17 to −12 ‰ when impacted by cement production emissions. Observation-based δ13Cm values derived by a moving Keeling-plot approach were in good agreement with the model-based estimates. They exhibited a larger scatter, while model-based estimates spread in a more narrow range. Overall, observation-based δ13Cm were limited to a smaller number of data points compared to model-based estimates owing to the stringent analysis prerequisites in combination with the low regional signal at JFJ.

<p>... more <p>With an increasing network of atmospheric stations that produce a constant data stream, top-down inverse transport modelling of GHGs in a quasi-operational way becomes feasible. The CarboScope-Regional inversion system embeds the regional inversion, within a global inversion using the two-step approach. The regional inversion consists of Lagrangian mesoscale transport from STILT, prior fluxes from the diagnostic VPRM biosphere model, and anthropogenic emissions from a combination of EDGAR v4.3 with the annually updated BP statistical report. Regional ocean fluxes were derived from the CarboScope ocean flux product based on SOCATv2019 data. The inversion uses atmospheric observations from 44 stations to infer biosphere-atmosphere exchange. The regional domain covers most of Europe (33 – 73N, 15W – 35E) with a spatial resolution of 0.25 degree for fluxes and 0.5 degree for flux corrections inferred by the inversion (i.e. the state space).<br>One of the critical parameters is the assumed uncertainty of the observations, and the major contribution to this is the model-data mismatch error, or representation error. Within CarboScope-Regional, this model-data mismatch error is specified differently for different station types, such as tall towers, mountain or coastal stations, etc. To evaluate the validity and appropriateness of these assumed uncertainties, a leave-one-out cross-validation is applied for a single year, using all stations except one for the inversion, and comparing posterior concentrations predicted for the omitted station with the observed concentrations. Results of this cross-validation will be presented separately for the different station types, and will be used to evaluate the magnitude of the assumed model-data mismatch errors.</p>

<p>... more <p>Regional flux estimates over Europe have been calculated using the two-step inverse system of the Jena CarboScope Regional inversion (CSR) to estimate the annual CO<sub>2</sub> budgets for recent years, in cooperation with the research project VERIFY. The CSR system assimilates observational datasets of CO<sub>2</sub> mixing ratio provided by the Integrated Carbon Observation System (ICOS) across the European domain to optimize Net Ecosystem Exchange (NEE) fluxes computed from biosphere models at a spatial resolution of 0.25 degree. Ocean fluxes are assumed to be constant over time. Fossil fuel emissions are obtained from EDGAR_v4.3 and updated based on British Petroleum (BP) statistics. Therefore, only biosphere-atmosphere exchange fluxes are considered to be optimized against the atmospheric data.</p><p>In this study we focus on the impact of using a-priori fluxes from different biosphere and ocean models on the annual CO<sub>2</sub> budget of posterior fluxes. Results calculated using the Vegetation and Photosynthesis Respiration Model (VPRM) and Simple Biosphere/Carnegie-Ames Stanford Approach (SiBCASA) models show a consistent posterior interannual variability, largely independent of which prior fluxes are used, even though those prior fluxes show considerable differences on annual scales.</p>

<p class=&... more <p class="p1"><span class="s1">Due to the growth of atmospheric methane and the remarkable uncertainties in its budget, there is a need to constrain the sources and sinks of this atmospheric tracer. Among the different regions emitting methane to the atmosphere, Africa has a considerable contribution to the global methane budget and has one of the largest associated uncertainties. Surface-based measurements could help to substantially diminish these uncertainties, but given the dearth of in-situ observations in most areas of Africa, satellite retrievals can be helpful to fill this gap. We use ground-based observations along with the SRON’s proxy and full physics XCH</span><span class="s2"><sub>4</sub></span><span class="s1"> products from the Greenhouse Gases Observing Satellite (GOSAT), and an inversion system consisting of the global 3-dimensional transport model TM3 as well as the high-resolution regional Stochastic Time-Inverted Lagrangian Transport model STILT to spatially resolve the regional emissions in Africa with a focus on the natural wetlands and also the oil and gas industries in Nigeria and Angola as the top oil-producing African countries. In this study, the global inversion is performed for 2009-2015 on a coarse resolution, ~ 3.83˚ x 5˚. The nominal spatial resolution of the regional inversion is 0.25˚ x 0.25˚ for 2011-2012. Prior fluxes for the nested run include the Emission Database for Global Atmospheric Research (EDGARv4.3.2) for anthropogenic sources including agriculture, and waste and energy, WetCHARTs wetlands ensemble, the Global Fire Assimilation System (GFAS) for biomass burning, Sanderson’s global database of termite methane emissions, and the soil Methanotrophy Model (MeMo) for the methane soil uptake. The significance of the petroleum industries’ emissions is examined by high-resolution inversions. Additionally, the consistency of the optimised fluxed derived from different types of measurements (e.g. surface-only, surface+satellite, satellite-only) is investigated and discussed.</span></p>

<p&amp... more <p>During May and June 2018, the intensive campaign CoMet (Carbon dioxide and Methane mission) made atmospheric measurements of greenhouse gases over Europe, with the upper Silesian coal basin (USCB) in southern Poland as a specific focus area. CoMet aimed at characterising the distribution of CH<sub>4</sub> and CO<sub>2</sub> over significant regional sources with the use of a fleet of research aircraft, as well as to validate remote sensing measurements from state-of-the-art instrumentation installed on-board against a set of independent in-situ observations.</p> <p>In order to link atmospheric mixing ratios to source emission rates, high-resolution simulations with WRF-GHG v 3.9.1.1. (10 km x10 km Europe + nested 2 km x 2 km domain over the USCB), driven by short-term meteorological forecasts from the ECMWF IFS model and forecasts from CAMS (Copernicus Atmospheric Monitoring Service) for initial and lateral tracer boundary conditions were performed. Biogenic fluxes of CO2 were calculated online using the VPRM model driven by MODIS indices. Anthropogenic emissions over Europe were taken from the database of TNO, Department of Climate, Air and Sustainability (7 km x 7 km), augmented with an internal emissions database developed within CoMet that uses coal mine ventilation shaft emission measurements in combination with recent updates of the E-PRTR (European Pollutant Release and Transfer Register).</p> <p>Tagged tracers were used to simulate a robust set of over 100 distinct anthropogenic sources of CH<sub>4</sub> and CO<sub>2</sub> from the study area, and these forward simulations were then used as the transport operator in an analytical Bayesian inversion system. Here we discuss the results of an analysis performed with the use of selected in-situ data measured over the course of the three-week campaign, including results and sensitivity tests.</p>

Atmospheric inversions are widely used in the optimization of surface carbon fluxes at regional s... more Atmospheric inversions are widely used in the optimization of surface carbon fluxes at regional scale using information from atmospheric CO 2 dry mole fractions. In many studies the prior flux uncertainty applied to the inversion schemes does not reflect directly the true flux uncertainties but it is used in such a way to regularize the inverse problem. Here, we aim to implement an inversion scheme using the Jena inversion system and applying a prior flux error structure derived from a model-data residual analysis using high spatial and temporal resolution over a full year period in the European domain. We analyzed the performance of the inversion system with a synthetic experiment, where the flux constraint is derived following the same residual analysis but applied to the model-model mismatch. The synthetic study showed a quite good agreement between posterior and "true" fluxes at European/Country and annual/monthly scales. Posterior monthly and country aggregated fluxes improved their correlation coefficient with the "known truth" by 7% compared to the prior estimates when compared to the reference, with a mean correlation of 0.92. Respectively, the ratio of the standard deviation between posterior/reference and prior/reference was also reduced by 33% with a mean value of 1.15. We identified temporal and spatial scales where the inversion system maximizes the derived information; monthly temporal scales at around 200 km spatial resolution seem to maximize the information gain.

Optimized biogenic carbon fluxes for Europe were estimated from high resolution regional scale in... more Optimized biogenic carbon fluxes for Europe were estimated from high resolution regional scale inversions, utilizing atmospheric CO 2 measurements at 16 stations for the year 2007. Additional sensitivity tests with different data-driven error structures were performed. As the atmospheric network is rather sparse and consequently contains large spatial gaps, we use a priori biospheric fluxes to further constrain the inversions. The biospheric fluxes were simulated by the Vegetation Photosynthesis and Respiration Model (VPRM) at a resolution of 0.1º and optimized against Eddy covariance data. Overall we estimate an a priori uncertainty of 0.54 GtC y-1 related to the poor spatial representation between the biospheric model and the ecosystem sites. The sink estimated from the atmospheric inversions for the area of Europe (as represented in the model domain) ranges between 0.23 and 0.38 GtC y-1 (0.30 and 0.49 GtC y-1 up-scaled to geographical Europe). This is within the range of posterior flux uncertainty estimates of previous studies using ground based observations.

Atmospheric Measurement Techniques Discussions

The carbon exchange between ecosystems and the atmosphere has a large influence on the Earth syst... more The carbon exchange between ecosystems and the atmosphere has a large influence on the Earth system and specifically on the climate. This exchange is therefore being studied intensively, often using the eddy covariance (EC) technique. EC measurements provide reliable results under turbulent atmospheric conditions, but under stable conditions-as they often occur at night-these measurements are known to misrepresent exchange fluxes. Nocturnal boundary layer (NBL) budgets can provide independent flux estimates under stable conditions, but their application so far has been limited by rather high cost and practical difficulties. Unmanned aircraft systems (UASs) equipped with trace gas analysers have the potential to make this method more accessible. We present the methodology and results of a proof of concept study carried out during the ScaleX 2016 campaign. Successive vertical profiles of carbon dioxide dry air mole fraction in the NBL were taken with a compact analyser carried by a UAS. We estimate an average carbon dioxide flux of 12 µmol • m −2 • s −1 , which is plausible for nocturnal respiration in this region in summer. Transport modelling suggests that the NBL budgets represent an area on the order of 100 km².

Atmospheric Chemistry and Physics

Optimized biogenic carbon fluxes for Europe were estimated from high-resolution regional-scale in... more Optimized biogenic carbon fluxes for Europe were estimated from high-resolution regional-scale inversions, utilizing atmospheric CO 2 measurements at 16 stations for the year 2007. Additional sensitivity tests with different datadriven error structures were performed. As the atmospheric network is rather sparse and consequently contains large spatial gaps, we use a priori biospheric fluxes to further constrain the inversions. The biospheric fluxes were simulated by the Vegetation Photosynthesis and Respiration Model (VPRM) at a resolution of 0.1 • and optimized against eddy covariance data. Overall we estimate an a priori uncertainty of 0.54 GtC yr −1 related to the poor spatial representation between the biospheric model and the ecosystem sites. The sink estimated from the atmospheric inversions for the area of Europe (as represented in the model domain) ranges between 0.23 and 0.38 GtC yr −1 (0.39 and 0.71 GtC yr −1 up-scaled to geographical Europe). This is within the range of posterior flux uncertainty estimates of previous studies using groundbased observations.

Atmospheric Chemistry and Physics

Atmospheric inversions are widely used in the optimization of surface carbon fluxes on a regional... more Atmospheric inversions are widely used in the optimization of surface carbon fluxes on a regional scale using information from atmospheric CO 2 dry mole fractions. In many studies the prior flux uncertainty applied to the inversion schemes does not directly reflect the true flux uncertainties but is used to regularize the inverse problem. Here, we aim to implement an inversion scheme using the Jena inversion system and applying a prior flux error structure derived from a model-data residual analysis using high spatial and temporal resolution over a full year period in the European domain. We analyzed the performance of the inversion system with a synthetic experiment, in which the flux constraint is derived following the same residual analysis but applied to the model-model mismatch. The synthetic study showed a quite good agreement between posterior and "true" fluxes on European, country, annual and monthly scales. Posterior monthly and country-aggregated fluxes improved their correlation coefficient with the "known truth" by 7 % compared to the prior estimates when compared to the reference, with a mean correlation of 0.92. The ratio of the SD between the posterior and reference and between the prior and reference was also reduced by 33 % with a mean value of 1.15. We identified temporal and spatial scales on which the inversion system maximizes the derived information; monthly temporal scales at around 200 km spatial resolution seem to maximize the information gain.

Journal of Chemistry, 2015

Polarization of atoms plays a substantial role in molecular interactions. Class I and II force fi... more Polarization of atoms plays a substantial role in molecular interactions. Class I and II force fields mostly calculate with fixed atomic charges which can cause inadequate descriptions for highly charged molecules, for example, ion channels or metalloproteins. Changes in charge distributions can be included into molecular mechanics calculations by various methods. Here, we present a very fast computational quantum mechanical method, the Bond Polarization Theory (BPT). Atomic charges are obtained via a charge calculation method that depend on the 3D structure of the system in a similar way as atomic charges ofab initiocalculations. Different methods of population analysis and charge calculation methods and their dependence on the basis set were investigated. A refined parameterization yielded excellent correlation ofR=0.9967. The method was implemented in the force field COSMOS-NMR and applied to the histidine-tryptophan-complex of the transmembrane domain of the M2 protein channel o...

Lagrangian Modeling of the Atmosphere, 2012

Journal of Geophysical Research, 2012

Tropical regions, especially the Amazon region, account for large emissions of methane (CH 4). He... more Tropical regions, especially the Amazon region, account for large emissions of methane (CH 4). Here, we present CH 4 observations from two airborne campaigns conducted within the BARCA (Balanço Atmosférico Regional de Carbono na Amazônia) project in the Amazon basin in November 2008 (end of the dry season) and May 2009 (end of the wet season). We performed continuous measurements of CH 4 onboard an aircraft for the first time in the Amazon region, covering the whole Amazon basin with over 150 vertical profiles between altitudes of 500 m and 4000 m. The observations support the finding of previous ground-based, airborne, and satellite measurements that the Amazon basin is a large source of atmospheric CH 4. Isotope analysis verified that the majority of emissions can be attributed to CH 4 emissions from wetlands, while urban CH 4 emissions could be also traced back to biogenic origin. A comparison of five TM5 based global CH 4 inversions with the observations clearly indicates that the inversions using SCIAMACHY observations represent the BARCA observations best. The calculated CH 4 flux estimate obtained from the mismatch between observations and TM5-modeled CH 4 fields ranges from 36 to 43 mg m À2 d À1 for the Amazon lowland region.

Atmospheric Chemistry and Physics, 2011

Accurate simulation of the spatial and temporal variability of tracer mixing ratios over complex ... more Accurate simulation of the spatial and temporal variability of tracer mixing ratios over complex terrain is challenging, but essential in order to utilize measurements made in complex orography (e.g. mountain and coastal sites) in an atmospheric inverse framework to better estimate regional fluxes of these trace gases. This study investigates the ability of high-resolution modeling tools to simulate meteorological and CO 2 fields around Ochsenkopf tall tower, situated in Fichtelgebirge mountain range-Germany (1022 m a.s.l.; 50 • 1 48" N, 11 • 48 30" E). We used tower measurements made at different heights for different seasons together with the measurements from an aircraft campaign. Two tracer transport models-WRF (Eulerian based) and STILT (Lagrangian based), both with a 2 km horizontal resolution-are used together with the satellite-based biospheric model VPRM to simulate the distribution of atmospheric CO 2 concentration over Ochsenkopf. The results suggest that the high-resolution models can capture diurnal, seasonal and synoptic variability of observed mixing ratios much better than coarse global models. The effects of mesoscale transports such as mountain-valley circulations and mountain-wave activities on atmospheric CO 2 distributions are reproduced remarkably well in the high-resolution models. With this study, we emphasize the potential of using high-resolution models in the context of inverse modeling frameworks to utilize measurements provided from mountain or complex terrain sites.

First results from EUROCOM is not better than that obtained in state-of-the-art global inversions... more First results from EUROCOM is not better than that obtained in state-of-the-art global inversions. However, more robust results are obtained for subregions within Europe, and in these areas with dense observational coverage, the objective of delivering robust countryscale flux estimates appears achievable in the near future.

Briefings in functional genomics & proteomics, 2007

The rapidly increasing amount of information on three-dimensional (3D) structures of biological m... more The rapidly increasing amount of information on three-dimensional (3D) structures of biological macro-molecules has still an insufficient impact on genome analysis, functional genomics and proteomics as well as on many other fields in biomedicine including disease-related research. There are, however, attempts to make structural data more easily accessible to the bench biologist. As members of the world-wide Protein Data Bank (wwPDB), the RCSB Protein Data Bank (PDB), the Protein Data Bank Japan and the Macromolecular Structure Database are the primary information resources for 3D structures of proteins, nucleic acids, carbohydrates and complexes thereof. In addition, a number of secondary resources have been set up that also provide information on all currently known structures in a relatively comprehensive manner and not focusing on specific features only. They include PDBsum, the OCA browser-database for protein structure/function, the Molecular Modeling Database and the Jena Lib...

Macromolecular Chemistry and Physics, 2000

. Static 13 C powder pattern of the carbons in cellulose II obtained from the crystal structure (... more . Static 13 C powder pattern of the carbons in cellulose II obtained from the crystal structure (thin line) and after time averaging of the tensors obtained by MD simulations (fat line).

Journal of Computational Chemistry, 1994

ABSTRACT Starting from the bond polarization theory (BPT), a new semiempirical method for the cal... more ABSTRACT Starting from the bond polarization theory (BPT), a new semiempirical method for the calculation of net atomic charges is developed. The bond polarization theory establishes a linear dependence of atomic charges from the bond polarization energy. This energy is calculated from the hybrid orbitals forming a bond and the point charges within the neighborhood. Empirical parameters are introduced for the polarity of an unpolarized bond and for the change of the atomic charge with σ- and π-bond polarization. Because these parameters are linear, they can be calibrated directly using net atomic charges from ab initio calculations. This procedure was performed using the charges from STO3G calculations on a set of 18 amino acids. Using the two parameters for CH, OH, σ-CO, and NH bonds and the three parameters for CC, CO, and CN bonds, the 350 ab initio charges can be reproduced with high accuracy by solving sets of linear equations for the charges. The calculation of charges for large molecular systems including all inter- and intramolecular mutual polarizations requires only a few seconds (up to 100 atoms) or minutes (700 atoms) on a PC. This procedure is well suited for the application in molecular mechanics or molecular dynamics programs to overcome the limitations of most force fields used up to now. One of the weakest points in these programs is the use of fixed or topological charges to define the electrostatic potential. As an application of the new method, we calculated the interaction energy of an ion with valinomycin. This ring molecule forms octahedral oxygen cages around ions like potassium and acts thereby as selective ion carrier. To accomplish this function, valinomycin has to strip off the hydratization spheres of the ions, and therefore its preference for certain types of ions could be deduced from the interaction energies. © 1994 by John Wiley & Sons, Inc.